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BUG: Two entity types, one biom_id: only last type is kept #1047

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arschat opened this issue Nov 4, 2024 · 0 comments
Open

BUG: Two entity types, one biom_id: only last type is kept #1047

arschat opened this issue Nov 4, 2024 · 0 comments
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@arschat
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arschat commented Nov 4, 2024

In which piece of software is this bug present?
ingest-api

Bug description/actual behaviour
When importing a spreadsheet in HCA's ingest, if I have two different type biomaterials with the same _id, ingest will create only one entity.

For example if I have a spreadsheet with specimen_from_organism.biomaterial_core.biomaterial_id and cell_suspension.biomaterial_core.biomaterial_id as sample_ID, ingest will create only one entity type i.e. cell suspension.

To Reproduce
Upload a spreadsheet with two different biomaterial entities, with identical biomaterial_id and observe the number of biomaterials entities.

Screenshot
specimen from organism ID
image

cell suspension IDs
image

biomaterials in ingest
image

Expected behavior
Ingest understands that the two biomaterials are different types and generates two different entities with the same *id.

Wrangler Note
Although we encourage contributors to use unique IDs across project, Tier 1 metadata encourage users to use "subject_id" as "sample_id" if only one sample is collected from donor.

This is the fundamental unit of sampling the tissue (the specimen taken from the subject), which can be the same as the 'subject_ID', but is often different if multiple samples are taken from the same subject.

Example submission: TestSameBiomaterialID - submission
minimum_test_sameID.xlsx

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